Tools that can benchmark cities, including cities in South East Europe, are necessary to enable the comparison and diffusion of more sustainable practices for urban systems. The “Sustainable Development of Energy, Water and Environment Systems Index” provides a composite indicator for benchmarking city performance based on 7 dimensions and 35 main indicators. In this research work, the Index is applied to a new sample of 18 cities in South East Europe for which data is collected, normalized, and aggregated. Klagenfurt (3.08), Velenje (3.06) and Pécs (3.01) are found to be the top three cities in the sample while an average city receives an index score of 2.85. The results are further compared to reference averages and evaluated based on the mean simulated values of 10,000 Monte Carlo experiments. The results are interpreted in quartiles for pioneering, transitioning, solution-seeking, and challenged cities. The results are then applied within a benchmarking tool of the Index that supports policy learning to trigger collaboration between cities and further used to match cities according to a search algorithm based on index performance. In addition, the results are compared to urban hierarchy as well as development contexts and mapped onto the spatial dimension as an initial step for enabling a “Sustainable Development of Energy, Water and Environment Systems Future City Network”. The paper concludes with a set of four proposed steps to enable decision-makers and urban planners in using the Sustainable Development of Energy, Water and Environment Systems Index in support of more sustainable urban systems.